Phylo: A Crowdsourced, Beautiful Biodiversity Game

European Honey Bee card. Image credit:

European Honey Bee card. Image credit:

They started with one provocative thought: “Kids know more about Pokemon than they do about the plants and animals in their backyard. We’d like to do something about that.”

And then the team behind the Science Creative Quarterly released the idea to the web to see what would happen. It was 2010.

Now, just a few years later, the resulting fruit of a crowdsourced labor is Phylo: The Trading Card Game. Phylo is a frankly beautiful, “sneakily educational”, immediately compelling and truly cross-functional collaboration of the artistic, gaming, scientific, education and even intellectual property law communities all coming together to create and curate a sort of “biodiversity Pokemon.”

Okay, sounds neat, but why?

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A Cup of Coffee, Hold the Rust

Rust on the underside of a coffee leaf.

Rust on the underside of a coffee leaf. Image used courtesy of Wikipedia.

While at my desk early in the day last week, one headline struck me as particularly troubling: “Coffee Rust Regains Foothold”.

Reports from the Institute of Coffee of Costa Rica estimate that the latest coffee outbreak may cut by 50% the 2013-14 coffee harvest in that country. Coffee specialists in the U.S. are calling it the worst outbreak of rust in Mexico and Central America since rust arrived in the region, 40-some years ago.

And in Kenya, Africa, coffee rust has been described as causing ever-greater problems, even with Kenyan coffee varieties resistant to rust being grown.

Several Central American governments are enacting special legislation to fund projects against spread of the fungus.

It’s early February and in this little corner of the world, times seem tough. We are suddenly (although typically, for southern Wisconsin, USA) getting regular snowfalls: 3” this day, 6” a day later. It adds up to a lot of shoveling.  There is nothing like a fresh snowfall and 30 minutes of shoveling to slow the morning commute. Continue reading

In Which I Tour a Cell Sorting Lab

Close up shot of the head of a FACS machine.

I recently had the chance to visit the core Flow Cytometry facility at the University of Alberta’s Faculty of Medicine and Dentistry, and to see a real FACS (Fluorescence Activated Cell Sorting) machine in action. Saturated as we are in technology that would have seemed miraculous even a decade ago, it’s sometimes hard for me to appreciate the sheer ingenuity of modern scientific apparatus. But somehow, stepping out of my familiar stomping grounds of smartphone programming, and seeing what we can now do with things in the real world instead of just ones and zeros, snapped me out of my complacency.

The facility supervisor – Dorothy Kratochwil-Otto, who kindly demonstrated the inner workings of one of the FACS machines as she spoke – explained to me in relative layman’s terms how the FACS technology works. Continue reading

How Is a Molecular Biologist Like a Computer Programmer?

My wife, the molecular biologist, tells me she spends her days “at the bench” and “in the hood.” There, she works with cells, plasmids, RNA, enzymes and buffers, incubators, water baths, columns, gels, filters and spectrophotometers. She transfers various quantities of liquids into and out of plastics and glassware. At least, that’s what I understand when I ask her, “how was your day?”

I can’t really understand her fascination with all of this, but then I don’t have to: I’m an app developer, a programmer who designs and builds applications for smartphones and tablets. My work day consists of sitting in front of a laptop, cranking out code. There’s the occasional break afforded by meetings and presentations, writing up design documents, sketching out how a user interface might look like. Then it’s back to the computer, and programming.

But in spite of these differences, there is a critical aspect of my wife’s work that, whenever she speaks of it, I immediately recognize in my own professional life: We both rely extensively on kits and components, and doing so profoundly affects the way that we approach our jobs. Continue reading

How a Musical Petri Dish Could Waste Your Whole Morning

You know those things you occasionally come across that look kind of cool and you think might be good for a minute or two of diversion? You know how it’s all fine and dandy until you somehow get sucked in and, before you know it, half the day is gone? Yeah. Meet Seaquence.

Seaquence is an online web app created by Ryan Alexander, Gabriel Dunne, and Daniel Massey, with support from Gray Area Foundation for the Arts. It is described as “an experiment in musical composition,” where “adopting a biological metaphor, you can create and combine musical lifeforms resulting in an organic, dynamic composition.” It’s basically an online petri dish where you add little squiggly creatures that make music. You control what combination of sounds each creature makes by adding antennae or changing the wiggle pattern of their bodies. When you’re done, you have a little virtual ambient orchestra; an ecosystem of minuscule musicians that you have guided, shaped and molded to your exact specifications. Oh, the power! Muaaa-haa-haa! Continue reading

Inviting Mother Nature to the design table

Marble globe on green leaf, close-upSustainability is all over the news these days. Green this, eco-friendly that, recycle everything, buy the twisty lightbulbs, and “Aren’t you going to compost that?” Much like good compost, sustainability is hot, and it’s finding its way not only into our households, but also into product design. Principles like using low-impact materials, energy efficiency and designing for reuse and renewability are increasing in importance. In ever-greater numbers, designers are looking to nature for inspiration as they create the next generation of innovative and sustainable products. It’s a burgeoning discipline called biomimicry. Continue reading

From Veggie Scraps to Humus: An Ecosystem in your Compost Bin

Living in the northern hemisphere where spring showers bring May flowers and being the first post in said month, I feel it is my duty to discuss an important topic: compost. Compost is the seemingly simple product of a complex mixture of materials. Take a smorgasbord of leaves, grass, kitchen waste, coffee grounds and other organic material, mix them into a pile or in a bin, and a dark, rich soil amendment is the end result. Thus, what many people label as waste becomes something quite useful if you want to grow vegetables, flowering plants or even a healthy lawn. (You do compost, don’t you?) Certainly my bleeding hearts appreciate a top dressing of compost in the spring to keep them vigorous, so much so that I had to split them only two years after planting them. But what does the work of converting a mess of green stuff and brown stuff to a crumbling, desirable end product?
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Mate Selection at Frog Cocktail Parties: Keep it Short, Low, Loud, and Stand Out from the Crowd (Oh, and have a colorful vocal sac, too)

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Hyla versicolor (Copes grey treefrog) Photo credit: LA Dawson wikipedia

Hyla versicolor (Copes grey treefrog) Photo credit: LA Dawson wikipedia

When I lived in Sioux City, IA, I had the opportunity of hanging out with a zoologist who studied the Plains Spadefoot Toad (Spea bombifrons). I would go out with her on nighttime listening surveys, and we would slowly drive the gravel farm roads in the middle of nowhere, weaving from one side to the other as we dodged hopping frogs and toads, and I would be amazed as the clamor of these calling anurans rattled my eardrums.

Just last week in Madison, as I took my lunchtime walk, I passed by a roadside wetland, and my ears filled with the calls of Chorus frogs, singing with all their one-inch might in hopes of attracting a mate. And, later that evening, as my daughter and I weeded our garden at home, I heard the crisp bell trill of two American toads carrying over the chorus frogs in the neighborhood.

Congresses of snoring Spadefoot Toads. In-your-face Copes Gray Tree Frogs. Peepers, Chorus Frogs and and Leopard Frogs. The evenings are noisy when the temperatures moderate and these frogs and toads come out to call. The din of the local roadside wetland begins to resemble the din of the local roadside bar, in more ways than one as it turns out. Continue reading

A Quick Method for A Tailing PCR Products

Some thermostable DNA polymerases, including Taq, add a single nucleotide base extension to the 3′ end of amplified DNA fragments. These polymerases usually add an adenine, leaving an “A” overhang. There are several approaches to overcome the cloning difficulties presented by the presence of A overhangs on PCR products. One method involves treating the product with Klenow to create a blunt-ended fragment for subcloning. Another choice is to add restriction sites to the ends of your PCR fragments. You can do this by incorporating the desired restriction sites into the PCR primers. After amplification, the PCR product is digested and subcloned into the cloning vector. Take care when using this method, as not all restriction enzymes efficiently cleave at the ends of DNA fragments, and you may not be able to use every restriction enzyme you desire. There is some useful information about cutting with restriction sites close to the end of linear fragments in the Restriction Enzyme Resource Guide. Also, some restriction enzymes require extra bases outside the recognition site, adding further expense to the PCR primers as well as risk of priming to unrelated sequences in the genome. Continue reading